A dye-binding assay for measurement of the binding of Cu(II) to proteins

Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.

Exploring the impact of mutation and post-translational modification on α-Synuclein: Insights from molecular dynamics simulations with and without copper

We report molecular dynamics simulations of two modifications to α-Synuclein, namely A53T mutation and phosphorylation at Ser129, which have been observed in Parkinson's disease patients. Both modifications are close to known metal binding sites, so as well as each modified peptide we also study Cu(II) bound to N-terminal and C-terminal residues. We show that A53T is predicted to cause increased β-sheet content of the peptide, with a persistent β-hairpin between residues 35-55 particularly notable. Phosphorylation has less effect on secondary structure but is predicted to significantly increase the size of the peptide, especially when bound to Cu(II), which is ascribed to reduced interaction of C-terminal sequence with central non-amyloid component. In addition, estimate of binding free energy to Cu(II) indicates A53T has little effect on metal-ion affinity, whereas phosphorylation markedly enhances the strength of binding. We suggest that the predicted changes in spatial extent and secondary structure of α-Synuclein may have implications for aggregation into Lewy bodies.

Sample Preparation and Protein Determination for 2D-DIGE Proteomics

Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a widely employed method for efficient protein separation and the determination of abundance changes in distinct proteoforms. This makes this gel-based method a key technique of comparative approaches in top-down proteomics. For the appropriate screening of proteome-wide alterations, initial preparative steps involve sample handling, homogenization, subcellular fractionation, and the determination of protein concentration, which makes the optimal application of these techniques a crucial part of a successful initiation of a new 2D-DIGE-based analysis. This chapter describes sample homogenization and a standardized protein assay for the preparation of homogenates with a known protein concentration for subsequent differential fluorescent tagging and two-dimensional gel electrophoretic separation.

Spectroscopic investigation on sonodynamic and sonocatalytic damage of BSA molecules by Thymol Blue (TB) derivants under ultrasonic irradiation

In this paper, the Thymol Blue derivants including Thymol Blue (thymolsulfonphthalein), Thymol Blue-DA (3,3'-Bis [N,N-bis (carboxymethyl) aminomethyl] thymolsulfonphthalein) and Thymol Blue-DA-Fe(III) (3,3'-Bis [N,N-bis (carboxymethyl) aminomethyl] thymolsulfonphthalein-Ferrous(III)) were adopted as sonosensitizers to study the sonodynamic and sonocatalytic activities under ultrasonic irradiation. At first, the interaction of Thymol Blue derivants with bovine serum albumin (BSA) was studied by fluorescence spectroscopy. On that basis, the sonodynamic and sonocatalytic damages of Thymol Blue derivants to BSA under ultrasonic irradiation were investigated by the combination of UV-vis, circular dichroism (CD) and fluorescence spectroscopy. Meanwhile, some influenced factors (ultrasonic irradiation time, Thymol Blue derivants concentration and ionic strength) on the damaging degree of BSA molecules were also reviewed. In addition, synchronous fluorescence spectra were used to estimate the binding and damage sites of Thymol Blue derivants to BSA. Finally, the generation of ROS during sonodynamic and sonocatalytic processes was confirmed by the method of Oxidation-Extraction Spectrometry (OEP). Perhaps, this paper may offer some important subjects for the study of Thymol Blue derivants in sonodynamic therapy (SDT) and sonocatalytic therapy (SCT) technologies for tumor treatment and the effect of the amino acid and central metal.

Analysis of beryllium to biomolecule binding using a metal specific fluorescent probe and competitive assay

Studying metal-biomolecule interactions is critical to the elucidation of the molecular basis of the biological functions and toxicity of metals. In the present study, a competitive fluorimetric approach has been developed to measure the apparent affinity of biomolecules for Be(2+) by using a Be(2+)-specific fluorigenic probe (10-hydroxybenzo[h]quinoline-7-sulfonate, HBQS). Under physiological conditions, HBQS coordinates with Be(2+) in a molar ratio of 1:1 and results in a fluorescence shift from 580 nm for HBQS to 480 nm for the Be-HBQS complex associated with significant fluorescence enhancement. When a beryllium ligand is present in the mixture of Be(2+) and HBQS, the competition of ligand against HBQS for beryllium ion binding results in dissociation and thus a fluorescence decrease of the Be-HBQS complex. By titrating ligand and monitoring the dose-dependent decrease of Be-HBQS complex fluorescence at 480 nm, the apparent affinity between ligand and Be(2+) can be derived. Applying this simple approach, the apparent affinities of various nucleotides and the iron-storage protein ferritin for beryllium ion have been determined. In particular, the apparent dissociation constant of Be(2+) and adenosine 5'-triphosphate (ATP) was also validated by an electrospray ionization mass spectrometric (ESI-MS) method. The general applicability of the proposed competition assay was further demonstrated using FluoZin-1, a zinc fluorescent indicator, in a binding study for Zn(2+) and bovine serum albumin. This newly developed competitive fluorimetric assay provides a sensitive, simple, and generic approach for affinity estimation of metal and biomolecule binding.